# Prompt-Guided Injection of Conformation to Pre-trained Protein Model

arXiv: https://arxiv.org/abs/2202.02944 · HTML: https://mlsanity.com/paper/2202.02944/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 46 references that are in the map.
- First posted on arXiv 7 Feb 2022.

## Builds on (most cited first, 19 of 19)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Prefix-Tuning: Optimizing Continuous Prompts for Generation](https://mlsanity.com/paper/2101.00190/) (2021)
- [The Power of Scale for Parameter-Efficient Prompt Tuning](https://mlsanity.com/paper/2104.08691/) (2021)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [fairseq: A Fast, Extensible Toolkit for Sequence Modeling](https://mlsanity.com/paper/1904.01038/) (2019)
- [Making Pre-trained Language Models Better Few-shot Learners](https://mlsanity.com/paper/2012.15723/) (2020)
- [Exploiting Cloze Questions for Few Shot Text Classification and Natural Language Inference](https://mlsanity.com/paper/2001.07676/) (2020)
- [GPT Understands, Too](https://mlsanity.com/paper/2103.10385/) (2021)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [WARP: Word-level Adversarial ReProgramming](https://mlsanity.com/paper/2101.00121/) (2021)
- [How Many Data Points is a Prompt Worth?](https://mlsanity.com/paper/2103.08493/) (2021)
- [ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing](https://mlsanity.com/paper/2007.06225/) (2020)
- [Differentiable Prompt Makes Pre-trained Language Models Better Few-shot Learners](https://mlsanity.com/paper/2108.13161/) (2021)
- [BERTology Meets Biology: Interpreting Attention in Protein Language Models](https://mlsanity.com/paper/2006.15222/) (2020)
- [ReCoSa: Detecting the Relevant Contexts with Self-Attention for Multi-turn Dialogue Generation](https://mlsanity.com/paper/1907.05339/) (2019)
- [Learning Unknown from Correlations: Graph Neural Network for Inter-novel-protein Interaction Prediction](https://mlsanity.com/paper/2105.06709/) (2021)

## Built on by (most cited first, 1 of 1)

- [Biological Sequence with Language Model Prompting: A Survey](https://mlsanity.com/paper/2503.04135/) (2025)

## Abstract (arXiv)

Pre-trained protein models (PTPMs) represent a protein with one fixed embedding and thus are not capable for diverse tasks. For example, protein structures can shift, namely protein folding, between several conformations in various biological processes. To enable PTPMs to produce task-aware representations, we propose to learn interpretable, pluggable and extensible protein prompts as a way of injecting task-related knowledge into PTPMs. In this regard, prior PTPM optimization with the masked language modeling task can be interpreted as learning a sequence prompt (Seq prompt) that enables PTPMs to capture the sequential dependency between amino acids. To incorporate conformational knowledge to PTPMs, we propose an interaction-conformation prompt (IC prompt) that is learned through back-propagation with the protein-protein interaction task. As an instantiation, we present a conformation-aware pre-trained protein model that learns both sequence and interaction-conformation prompts in a multi-task setting. We conduct comprehensive experiments on nine protein datasets. Results confirm our expectation that using the sequence prompt does not hurt PTPMs' performance on sequence-related tasks while incorporating the interaction-conformation prompt significantly improves PTPMs' performance on tasks where conformational knowledge counts. We also show the learned prompts can be combined and extended to deal with new complex tasks.